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fix TRZ file reader on big-endian architectures #1425

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wants to merge 12 commits into from
Closed

fix TRZ file reader on big-endian architectures #1425

wants to merge 12 commits into from

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rathann
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@rathann rathann commented Jun 22, 2017

Fixes #1424 .

Changes made in this Pull Request:

  • all ints and floats should be read as little-endian from TRZ files

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

rathann and others added 12 commits June 9, 2017 11:45
@rathann
use correct int types
51649ad 
This fixes ERRORs and FAILs in the testsuite on 32bit:

TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

and

assert_(out[0].dtype == np.int64)
  File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 92, in assert_
    raise AssertionError(smsg)
AssertionError
@rathann
relax test_symmetry test due to lower precision on 32bit
280dc13
@richardjgowers @rathann
Aesthetic fixes to test_gro
1f61efd 
Removed TestCase usage
@richardjgowers @rathann
Added tests for issue #1395
b3adb1b
@richardjgowers @rathann
Added lib.util.ltruncate_integer
6baf47e
@richardjgowers @rathann
Changed coordinate writers to use ltruncate_int
46768e5 
Fixes issue #1395
@richardjgowers @rathann
More work on making indexing arrays use intp (#1362)
6a3e427 
- Added tests for 32 bit index support
- added @rathann to AUTHORS
@jbarnoud @rathann
Explicitly define __hash__ for groups
9a34b0f 
Groups (AtomGroup, ResidueGroup, SegmentGroup) cannot be stored in sets
or used as dict key if they are not hashable. In python 3, the __hash__
method is not defined implicitly anymore when a class has a __eq__ method.

Fixes #1397
@rathann
Merge remote-tracking branch 'upstream/develop' into develop
180216f
@rathann
fix int type in asserts in TestDownshiftArrays
059f664 
this was missed in eed7761
@rathann
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
b9084b0 
…to develop
@rathann
fix TRZ file reader on big-endian arches
efa4628 
Numpy dtype int (iN) and float (fN) specifiers assume native-endian
by default, so force them to be little-endian.

Closes #1424.
@kain88-de
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@rathann your git history seems to be a bit confused. Do you mind cleanint it up. It seems to be that you only want to add the last commit. I recommend to use feature branches in your own repository to keep these things from happening.

@rathann
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rathann commented Jun 22, 2017

@kain88-de Yes, sorry. I'll try, though I'm not quite sure how to do it. Feel free to reject this PR and just cherry-pick the last commit.

@kain88-de
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@rathann can you please include a CHANGELOG entry and a comment in the docs that MDAnalysis expects little endian trz files.

@orbeckst
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Yes, sorry. I'll try, though I'm not quite sure how to do it. Feel free to reject this PR and just cherry-pick the last commit.

In general:

git checkout develop
git pull
git checkout -b fix-trz-endian   # create feature branch
# hack and add on your branch
# ...
git add package/MDAnalysis/coordinates/TRZ.py
git commit ...
git push -u origin fix-trz-endian

and then do the PR. Typically, don't merge develop into your branch if you can avoid it because we often use squash and that does not always works well with merges.

@orbeckst orbeckst mentioned this pull request Jun 22, 2017
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@orbeckst
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I am replacing this PR with #1427.

@orbeckst orbeckst closed this Jun 22, 2017
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@rathann @kain88-de @orbeckst @richardjgowers @jbarnoud